Contacts of the helix formed by residues 277 - 291 (chain C) in PDB entry 2PGW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 277 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C SER* 3.7 14.1 - - - +
110C ASP* 3.5 9.2 - - - -
111C MSE 6.0 0.2 - - - -
272C PRO* 2.9 20.7 + - - +
275C ILE* 3.6 1.9 - - - +
276C GLY* 1.3 79.4 - - - +
278C ILE* 1.3 64.7 + - - -
280C PRO* 3.4 4.3 - - - -
281C MSE 3.2 27.5 + - - +
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Residues in contact with ILE 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ASP* 2.7 13.2 + - - +
111C MSE 4.1 22.4 - - + -
114C TRP* 4.2 19.5 - - + -
125C VAL* 4.4 8.1 - - + -
129C LEU* 3.7 28.7 - - + -
272C PRO* 5.3 1.8 - - + -
277C GLY* 1.3 69.8 - - - -
279C GLN* 1.3 65.8 + - - +
281C MSE 3.1 18.4 + - - +
282C MSE 3.3 8.4 + - + +
309C ALA* 4.2 12.6 - - + +
312C HIS* 5.8 0.2 - - + -
313C ILE* 3.6 33.4 - - + -
356C LEU* 3.9 28.3 - - + -
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Residues in contact with GLN 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 4.1 4.3 - - - +
80C ALA* 3.5 26.8 - - - +
110C ASP* 3.2 5.4 + - - +
114C TRP* 3.5 34.8 - - + +
129C LEU* 5.5 4.1 - - + +
278C ILE* 1.3 79.6 - - - +
280C PRO* 1.3 71.1 - - + +
282C MSE 3.0 26.2 + - + +
283C LYS* 3.3 17.2 + - + +
129F LEU* 3.1 31.3 + - - +
130F GLY* 3.9 1.4 - - - -
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Residues in contact with PRO 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ILE* 6.5 0.7 - - + -
110C ASP* 3.9 5.8 - - - +
275C ILE* 3.4 40.2 - - + +
276C GLY* 3.6 17.5 - - - +
277C GLY* 3.4 14.8 - - - -
278C ILE 3.7 0.4 - - - +
279C GLN* 1.3 95.0 - - + +
281C MSE 1.3 60.4 + - - +
283C LYS* 3.0 19.0 + - + +
284C ALA 2.9 18.0 + - - -
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Residues in contact with MSE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ILE* 3.3 35.2 - - + +
271C GLY* 3.6 15.9 - - - -
272C PRO 3.9 4.9 - - - -
275C ILE* 3.6 19.3 - - + -
277C GLY 3.2 18.1 + - - +
278C ILE 3.1 10.4 + - - +
280C PRO* 1.3 78.6 - - - +
282C MSE 1.3 60.1 + - - +
284C ALA* 3.2 4.3 + - + +
285C ALA* 2.9 30.5 + - - +
295C ILE* 3.7 24.7 - - + -
297C ILE* 4.5 6.3 - - + -
313C ILE* 3.9 31.2 - - + -
317C ILE* 4.0 14.8 - - + +
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Residues in contact with MSE 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LEU* 4.2 25.6 - - + +
278C ILE 3.7 14.6 - - - +
279C GLN* 3.0 17.1 + - + +
281C MSE 1.3 77.4 - - - +
283C LYS* 1.3 58.5 + - + +
285C ALA* 3.4 6.0 + - - +
286C ALA* 3.1 26.7 + - - +
313C ILE* 3.4 43.3 - - + +
316C ALA* 3.7 26.9 - - + +
317C ILE* 3.5 21.3 - - + -
283F LYS* 5.7 1.0 - - - +
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Residues in contact with LYS 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C LEU* 3.9 19.7 - - + +
279C GLN* 3.3 16.8 + - + +
280C PRO* 3.0 20.2 + - + +
282C MSE 1.3 76.6 - - + +
284C ALA* 1.3 64.8 + - - +
286C ALA* 3.3 4.8 + - - +
287C VAL* 3.2 26.2 + - - +
282F MSE 5.7 0.7 - - - +
286F ALA* 3.8 22.8 - - + +
289F GLU* 2.8 35.6 + - - +
318F PRO* 4.2 15.4 - - - +
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Residues in contact with ALA 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LEU* 4.0 9.1 - - - +
256C VAL* 4.0 27.7 - - + +
270C ILE* 4.6 16.4 - - + -
275C ILE* 4.3 13.0 - - + -
280C PRO 2.9 12.0 + - - +
281C MSE 3.2 11.4 + - + +
283C LYS* 1.3 75.5 - - - +
285C ALA* 1.3 64.6 + - - +
287C VAL* 3.2 5.2 + - - +
288C ALA* 3.0 22.9 + - - +
295C ILE* 4.6 3.1 - - + -
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C MSE 2.9 16.8 + - - +
282C MSE 3.5 7.9 - - - +
284C ALA* 1.3 77.1 - - - +
286C ALA* 1.3 57.1 + - - +
288C ALA 3.4 0.3 + - - -
289C GLU* 2.8 27.4 + - - +
295C ILE* 3.8 13.8 - - + +
317C ILE* 3.9 39.9 - - + -
318C PRO* 5.4 2.7 - - + -
319C ASN* 3.2 12.3 + - - +
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C MSE 3.1 14.0 + - - +
283C LYS* 3.6 10.5 - - - +
284C ALA 3.2 0.2 - - - -
285C ALA* 1.3 73.1 - - - +
287C VAL* 1.3 67.2 + - - +
289C GLU* 3.3 11.4 + - - +
290C ALA* 2.9 24.9 + - - +
253F LEU* 4.2 3.9 - - + +
283F LYS* 3.9 46.7 - - + +
286F ALA* 4.7 2.5 - - + -
287F VAL* 4.2 2.6 - - + +
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Residues in contact with VAL 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C LEU* 3.9 18.6 - - + +
256C VAL* 4.0 11.4 - - + -
257C TYR* 3.9 37.7 - - + -
260C CYS* 4.2 7.4 - - + -
283C LYS 3.2 13.2 + - - +
284C ALA 3.2 7.7 + - - +
286C ALA* 1.3 75.3 - - - +
288C ALA* 1.3 63.1 + - - +
290C ALA* 3.3 4.5 + - - +
291C ALA* 3.1 19.9 + - - +
257F TYR* 4.8 4.0 - - + -
286F ALA 4.3 1.1 - - - +
287F VAL* 4.1 24.9 - - + +
290F ALA* 4.2 13.7 - - + -
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C VAL* 4.6 0.4 - - + +
260C CYS* 3.9 12.5 - - - -
268C ILE* 4.6 9.0 - - + -
284C ALA 3.0 13.2 + - - +
285C ALA 3.7 6.7 - - - +
287C VAL* 1.3 77.1 - - - +
289C GLU* 1.3 61.2 + - - +
291C ALA* 2.9 10.0 + - - +
293C LEU* 2.9 44.8 + - + +
294C LYS 4.7 0.2 - - - +
295C ILE* 3.9 19.1 - - + -
319C ASN* 3.8 4.3 - - - +
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Residues in contact with GLU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C ALA 2.8 18.2 + - - +
286C ALA* 3.5 5.7 - - - +
288C ALA* 1.3 75.6 - - - +
290C ALA* 1.3 62.0 + - - +
292C GLY* 3.0 13.3 + - - -
293C LEU 3.8 3.4 - - - +
318C PRO* 4.0 19.9 - - - +
319C ASN* 3.3 20.7 - - + +
253F LEU* 4.0 10.3 - - + +
254F TYR* 3.4 26.7 + - - +
283F LYS* 2.7 38.4 + - - -
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B SER* 4.5 3.3 + - - -
286C ALA 2.9 17.4 + - - +
287C VAL 3.5 5.8 - - - +
289C GLU* 1.3 76.2 - - - +
291C ALA* 1.3 58.9 + - - +
292C GLY 3.3 0.4 + - - -
253F LEU* 3.8 20.8 - - + +
254F TYR* 3.2 27.3 - - - -
257F TYR* 3.6 36.1 - - + -
287F VAL* 4.1 9.9 - - + -
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B SER* 3.7 8.3 + - - -
260C CYS* 3.6 37.9 - - + -
263C ARG* 2.8 35.4 + - - +
287C VAL 3.1 5.9 + - - +
288C ALA 2.9 9.2 + - - +
290C ALA* 1.3 76.2 - - - +
292C GLY* 1.3 62.1 + - - +
293C LEU* 3.6 3.5 + - + +
257F TYR* 3.7 19.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il